SERIAL CLONER 2.1 May Handling Features/Annotations

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1 SERIAL CLONER 2.1 May 2010 Handling Features/Annotations Since version 2.0, Serial Cloner handles annotations and features. Here are some descriptions and hints about these new possibilities. The symbol indicate that this function has been added or updated in V2.1 I. Accessing features in the Sequence window A new tab has been added (Features) that gives access to features characteristics and management. A list of Features is shown on the left; double clicking on one will select the corresponding nucleotide sequence. To edit (add/delete/modify) Features, one has to be in the 'Edit' mode. The Edit button is used to toggle between the 'protected' mode where no unwanted modification can be done and the 'Edit' mode. One can select whether a feature will actually be displayed on the map (using the 'Show' checkbox). Shown features are listed in Bold characters. To decide to Show or Hide all features at once, press the [ALT] key before clicking on the checkbox. A feature can have or not a pointing arrow ('Arrow' checkbox). To change the Feature color, click on the colored box and select another color. The order in the list dictate the order by which Features will be drawn, and this can be important in case they overlap. To alter the order simply drag the Feature at another position in the list. The + and button are used to add and delete a Feature respectively. A pop-up message will ask for confirmation before deleting a Feature (there is no undo). This pop-message can be avoided if you press the [ALT] key before clicking on the button. The button then gets red to indicate that no confirmation will be asked for. This is particularly useful when deleting multiple Features. II. Display of Features in the Sequence Window Features are visible in color in the sequence window. It is possible to show/hide them using the 'Show Features' checkbox.

2 When the insertion point is located within a Feature, the corresponding Feature's name is indicated above the Sequence Field. NB: note that since version 2.1 it is now possible to change the Sequence window size (as well as the character size under Windows AND MacOSX). The scrolling of the sequence when selecting has also been improved. III. Graphical display of Feature. Features can be displayed in the Graphic Map. They are represented by colored boxes with or without a pointing arrow. It is possible to switch between a Graphic Map with and without Feature using the checkbox present in the top left of the window ('Features'). A simple click on a Feature name selects the corresponding portion in the map. A double Click selects the corresponding sequence in the parent Sequence Window. 2

3 Note that it is now possible (since V2.0) to move the Restriction site and Features name boxes to highlight some of them before printing or copying the map. It is also possible to display only certain sites together with the Features. Finally, it is now possible (since v2.0) to resize the Graphic map in Height AND Width. 3

4 IV. Text visualization of the Features With Serial Cloner 2.1, it is now possible to see the Features with the Sequence Map. A checkbox present at the top left of the Sequence Map window allows to toggle on and off Feature display. The ">" and "<" is used to indicated the sense of the Feature. A legend is pasted at the end of the map. <Serial Cloner V2.1> -- <2 mai :59> Restriction map of pbluescript II SK(+) Showing restriction enzymes cutting maximum 1 time [using RELibrary as a Restriction Enzyme Library] ### PsiI CTAAATTGTAAGCGTTAATATTTTGTTAAAATTCGCGTTAAATTTTTGTTAAATCAGCTCATTTTTTAACCAATAGGCCGAAATCGGCAAAATCCCTTAT < 100 L N C K R * Y F V K I R V K F L L N Q L I F * P I G R N R Q N P L * * I V S V N I L L K F A L N F C * I S S F F N Q * A E I G K I P Y K L * A L I F C * N S R * I F V K S A H F L T N R P K S A K S L I GATTTAACATTCGCAATTATAAAACAATTTTAAGCGCAATTTAAAAACAATTTAGTCGAGTAAAAAATTGGTTATCCGGCTTTAGCCGTTTTAGGGAATA >AloI AAATCAAAAGAATAGACCGAGATAGGGTTGAGTGTTGTTCCAGTTTGGAACAAGAGTCCACTATTAAAGAACGTGGACTCCAACGTCAAAGGGCGAAAAA < 200 I K R I D R D R V E C C S S L E Q E S T I K E R G L Q R Q R A K N K S K E * T E I G L S V V P V W N K S P L L K N V D S N V K G R K T N Q K N R P R * G * V L F Q F G T R V H Y * R T W T P T S K G E K TTTAGTTTTCTTATCTGGCTCTATCCCAACTCACAACAAGGTCAAACCTTGTTCTCAGGTGATAATTTCTTGCACCTGAGGTTGCAGTTTCCCGCTTTTT BsaAI >BtgZI DraIII >F1 ori CCGTCTATCAGGGCGATGGCCCACTACGTGAACCATCACCCTAATCAAGTTTTTTGGGGTCGAGGTGCCGTAAAGCACTAAATCGGAACCCTAAAGGGAG < 300 R L S G R W P T T * T I T L I K F F G V E V P * S T K S E P * R E V Y Q G D G P L R E P S P * S S F L G S R C R K A L N R N P K G S P S I R A M A H Y V N H H P N Q V F W G R G A V K H * I G T L K G A GGCAGATAGTCCCGCTACCGGGTGATGCACTTGGTAGTGGGATTAGTTCAAAAAACCCCAGCTCCACGGCATTTCGTGATTTAGCCTTGGGATTTCCCTC NaeI NgoMIV CCCCCGATTTAGAGCTTGACGGGGAAAGCCGGCGAACGTGGCGAGAAAGGAAGGGAAGAAAGCGAAAGGAGCGGGCGCTAGGGCGCTGGCAAGTGTAGCG < 400 P P I * S L T G K A G E R G E K G R E E S E R S G R * G A G K C S G P R F R A * R G K P A N V A R K E G K K A K G A G A R A L A S V A P D L E L D G E S R R T W R E R K G R K R K E R A L G R W Q V * R GGGGGCTAAATCTCGAACTGCCCCTTTCGGCCGCTTGCACCGCTCTTTCCTTCCCTTCTTTCGCTTTCCTCGCCCGCGATCCCGCGACCGTTCACATCGC <BsmFI <LacZ alpha GTCACGCTGCGCGTAACCACCACACCCGCCGCGCTTAATGCGCCGCTACAGGGCGCGTCCCATTCGCCATTCAGGCTGCGCAACTGTTGGGAAGGGCGAT < 500 H A A R N H H T R R A * C A A T G R V P F A I Q A A Q L L G R A I V T L R V T T T P A A L N A P L Q G A S H S P F R L R N C W E G R S S R C A * P P H P P R L M R R Y R A R P I R H S G C A T V G K G D CAGTGCGACGCGCATTGGTGGTGTGGGCGGCGCGAATTACGCGGCGATGTCCCGCGCAGGGTAAGCGGTAAGTCCGACGCGTTGACAACCCTTCCCGCTA CGGTGCGGGCCTCTTCGCTATTACGCCAGCTGGCGAAAGGGGGATGTGCTGCAAGGCGATTAAGTTGGGTAACGCCAGGGTTTTCCCAGTCACGACGTTG < 600 G A G L F A I T P A G E R G M C C K A I K L G N A R V F P V T T L V R A S S L L R Q L A K G G C A A R R L S W V T P G F S Q S R R C R C G P L R Y Y A S W R K G D V L Q G D * V G * R Q G F P S H D V V GCCACGCCCGGAGAAGCGATAATGCGGTCGACCGCTTTCCCCCTACACGACGTTCCGCTAATTCAACCCATTGCGGTCCCAAAAGGGTCAGTGCTGCAAC PssI PspOMI EcoO109I SalI Acc65I SciI HincII EcoRV >M13-fwd >T7 KpnI ApaI XhoI AccI ClaI HindIII TAAAACGACGGCCAGTGAGCGCGCGTAATACGACTCACTATAGGGCGAATTGGGTACCGGGCCCCCCCTCGAGGTCGACGGTATCGATAAGCTTGATATC < 700 * N D G Q * A R V I R L T I G R I G Y R A P P R G R R Y R * A * Y R K T T A S E R A * Y D S L * G E L G T G P P L E V D G I D K L D I K R R P V S A R N T T H Y R A N W V P G P P S R S T V S I S L I S ATTTTGCTGCCGGTCACTCGCGCGCATTATGCTGAGTGATATCCCGCTTAACCCATGGCCCGGGGGGGAGCTCCAGCTGCCATAGCTATTCGAACTATAG BtgI SmaI SacII PstI UthSI SpeI EagI AleI EcoICRI EcoRI XmaI BamHI XbaI NotI BstXI SacI <T3 GAATTCCTGCAGCCCGGGGGATCCACTAGTTCTAGAGCGGCCGCCACCGCGGTGGAGCTCCAGCTTTTGTTCCCTTTAGTGAGGGTTAATTGCGCGCTTG < 800 I P A A R G I H * F * S G R H R G G A P A F V P F S E G * L R A W E F L Q P G G S T S S R A A A T A V E L Q L L F P L V R V N C A L G 4

5 N S C S P G D P L V L E R P P P R W S S S F C S L * * G L I A R L CTTAAGGACGTCGGGCCCCCTAGGTGATCAAGATCTCGCCGGCGGTGGCGCCACCTCGAGGTCGAAAACAAGGGAAATCACTCCCAATTAACGCGCGAAC <M13-rev <LacO GCGTAATCATGGTCATAGCTGTTTCCTGTGTGAAATTGTTATCCGCTCACAATTCCACACAACATACGAGCCGGAAGCATAAAGTGTAAAGCCTGGGGTG < 900 R N H G H S C F L C E I V I R S Q F H T T Y E P E A * S V K P G V V I M V I A V S C V K L L S A H N S T Q H T S R K H K V * S L G C A * S W S * L F P V * N C Y P L T I P H N I R A G S I K C K A W G A CGCATTAGTACCAGTATCGACAAAGGACACACTTTAACAATAGGCGAGTGTTAAGGTGTGTTGTATGCTCGGCCTTCGTATTTCACATTTCGGACCCCAC CCTAATGAGTGAGCTAACTCACATTAATTGCGTTGCGCTCACTGCCCGCTTTCCAGTCGGGAAACCTGTCGTGCCAGCTGCATTAATGAATCGGCCAACG < 1000 P N E * A N S H * L R C A H C P L S S R E T C R A S C I N E S A N A L M S E L T H I N C V A L T A R F P V G K P V V P A A L M N R P T * * V S * L T L I A L R S L P A F Q S G N L S C Q L H * * I G Q R GGATTACTCACTCGATTGAGTGTAATTAACGCAACGCGAGTGACGGGCGAAAGGTCAGCCCTTTGGACAGCACGGTCGACGTAATTACTTAGCCGGTTGC >SapI CGCGGGGAGAGGCGGTTTGCGTATTGGGCGCTCTTCCGCTTCCTCGCTCACTGACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCAC < 1100 R G E A V C V L G A L P L P R S L T R C A R S F G C G E R Y Q L T R G E R R F A Y W A L F R F L A H * L A A L G R S A A A S G I S S L A G R G G L R I G R S S A S S L T D S L R S V V R L R R A V S A H GCGCCCCTCTCCGCCAAACGCATAACCCGCGAGAAGGCGAAGGAGCGAGTGACTGAGCGACGCGAGCCAGCAAGCCGACGCCGCTCGCCATAGTCGAGTG PciI NspI AflIII TCAAAGGCGGTAATACGGTTATCCACAGAATCAGGGGATAACGCAGGAAAGAACATGTGAGCAAAAGGCCAGCAAAAGGCCAGGAACCGTAAAAAGGCCG < 1200 Q R R * Y G Y P Q N Q G I T Q E R T C E Q K A S K R P G T V K R P K G G N T V I H R I R G * R R K E H V S K R P A K G Q E P * K G R S K A V I R L S T E S G D N A G K N M * A K G Q Q K A R N R K K A A AGTTTCCGCCATTATGCCAATAGGTGTCTTAGTCCCCTATTGCGTCCTTTCTTGTACACTCGTTTTCCGGTCGTTTTCCGGTCCTTGGCATTTTTCCGGC CGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATA < 1300 R C W R F S I G S A P L T S I T K I D A Q V R G G E T R Q D Y K D T V A G V F P * A P P P * R A S Q K S T L K S E V A K P D R T I K I L L A F F H R L R P P D E H H K N R R S S Q R W R N P T G L * R Y GCAACGACCGCAAAAAGGTATCCGAGGCGGGGGGACTGCTCGTAGTGTTTTTAGCTGCGAGTTCAGTCTCCACCGCTTTGGGCTGTCCTGATATTTCTAT CCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCG < 1400 R R F P L E A P S C A L L F R P C R L P D T C P P F S L R E A W R P G V S P W K L P R A L S C S D P A A Y R I P V R L S P F G K R G A Q A F P P G S S L V R S P V P T L P L T G Y L S A F L P S G S V A GGTCCGCAAAGGGGGACCTTCGAGGGAGCACGCGAGAGGACAAGGCTGGGACGGCGAATGGCCTATGGACAGGCGGAAAGAGGGAAGCCCTTCGCACCGC <BseYI CTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCG < 1500 F L I A H A V G I S V R C R S F A P S W A V C T N P P F S P T A A F S * L T L * V S Q F G V G R S L Q A G L C A R T P R S A R P L R L S H S S R C R Y L S S V * V V R S K L G C V H E P P V Q P D R C A GAAAGAGTATCGAGTGCGACATCCATAGAGTCAAGCCACATCCAGCAAGCGAGGTTCGACCCGACACACGTGCTTGGGGGGCAAGTCGGGCTGGCGACGC <ColE1 origin AlwNI CCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGT < 1600 P Y P V T I V L S P T R * D T T Y R H W Q Q P L V T G L A E R G M * L I R * L S S * V Q P G K T R L I A T G S S H W * Q D * Q S E V C L S G N Y R L E S N P V R H D L S P L A A A T G N R I S R A R Y V GGAATAGGCCATTGATAGCAGAACTCAGGTTGGGCCATTCTGTGCTGAATAGCGGTGACCGTCGTCGGTGACCATTGTCCTAATCGTCTCGCTCCATACA AGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGA < 1700 A V L Q S S * S G G L T T A T L E G Q Y L V S A L C * S Q L P S E R R C Y R V L E V V A * L R L H * K D S I W Y L R S A E A S Y L R K G G A T E F L K W W P N Y G Y T R R T V F G I C A L L K P V T F G TCCGCCACGATGTCTCAAGAACTTCACCACCGGATTGATGCCGATGTGATCTTCCTGTCATAAACCATAGACGCGAGACGACTTCGGTCAATGGAAGCCT AAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTC < 1800 K E L V A L D P A N K P P L V A V V F L F A S S R L R A E K K D L K S W * L L I R Q T N H R W * R W F F C L Q A A D Y A Q K K R I S K R V G S S * S G K Q T T A G S G G F F V C K Q Q I T R R K K G S Q TTTTCTCAACCATCGAGAACTAGGCCGTTTGTTTGGTGGCGACCATCGCCACCAAAAAAACAAACGTTCGTCGTCTAATGCGCGTCTTTTTTTCCTAGAG

6 AAGAAGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCAC < 1900 K K I L * S F L R G L T L S G T K T H V K G F W S * D Y Q K G S S P R R S F D L F Y G V * R S V E R K L T L R D F G H E I I K K D L H E D P L I F S T G S D A Q W N E N S R * G I L V M R L S K R I F T TTCTTCTAGGAAACTAGAAAAGATGCCCCAGACTGCGAGTCACCTTGCTTTTGAGTGCAATTCCCTAAAACCAGTACTCTAATAGTTTTTCCTAGAAGTG CTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCT < 2000 R S F * I K N E V L N Q S K V Y M S K L G L T V T N A * S V R H L L D P F K L K M K F * I N L K Y I * V N L V * Q L P M L N Q * G T Y * I L L N * K * S F K S I * S I Y E * T W S D S Y Q C L I S E A P GATCTAGGAAAATTTAATTTTTACTTCAAAATTTAGTTAGATTTCATATATACTCATTTGAACCAGACTGTCAATGGTTACGAATTAGTCACTCCGTGGA >HaeIV AhdI ATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTG < 2100 S Q R S V Y F V H P * L P D S P S C R * L R Y G R A Y H L A P V L L S D L S I S F I H S C L T P R R V D N Y D T G G L T I W P Q C C I S A I C L F R S S I V A * L P V V * I T T I R E G L P S G P S A A TAGAGTCGCTAGACAGATAAAGCAAGTAGGTATCAACGGACTGAGGGGCAGCACATCTATTGATGCTATGCCCTCCCGAATGGTAGACCGGGGTCACGAC <BsaI CAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATC < 2200 Q * Y R E T H A H R L Q I Y Q Q * T S Q P E G P S A E V V L Q L Y P N D T A R P T L T G S R F I S N K P A S R K G R A Q K W S C N F I M I P R D P R S P A P D L S A I N Q P A G R A E R R S G P A T L S GTTACTATGGCGCTCTGGGTGCGAGTGGCCGAGGTCTAAATAGTCGTTATTTGGTCGGTCGGCCTTCCCGGCTCGCGTCTTCACCAGGACGTTGAAATAG CGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTG < 2300 P P S S L L I V A G K L E * V V R Q L I V C A T L L P L L Q A S W R L H P V Y * L L P G S * S K * F A S * * F A Q R C C H C Y R H R G A S I Q S I N C C R E A R V S S S P V N S L R N V V A I A T G I V GCGGAGGTAGGTCAGATAATTAACAACGGCCCTTCGATCTCATTCATCAAGCGGTCAATTATCAAACGCGTTGCAACAACGGTAACGATGTCCGTAGCAC <AmpR GTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCT < 2400 C H A R R L V W L H S A P V P N D Q G E L H D P P C C A K K R L A V T L V V W Y G F I Q L R F P T I K A S Y M I P H V V Q K S G * L V S R S S F G M A S F S S G S Q R S R R V T * S P M L C K K A V S S CACAGTGCGAGCAGCAAACCATACCGAAGTAAGTCGAGGCCAAGGGTTGCTAGTTCCGCTCAATGTACTAGGGGGTACAACACGTTTTTTCGCCAATCGA CCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGT < 2500 P S V L R S L S E V S W P Q C Y H S W L W Q H C I I L L L S C H P * L R S S D R C Q K * V G R S V I T H G Y G S T A * F S Y C H A I R F G P P I V V R S K L A A V L S L M V M A A L H N S L T V M P S V GGAAGCCAGGAGGCTAGCAACAGTCTTCATTCAACCGGCGTCACAATAGTGAGTACCAATACCGTCGTGACGTATTAAGAGAATGACAGTACGGTAGGCA TatI >BcgI ScaI >BcgI BsaHI AAGATGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAATACGGGATAAT < 2600 D A F L * L V S T Q P S H S E N S V C G D R V A L A R R Q Y G I I K M L F C D W * V L N Q V I L R I V Y A A T E L L L P G V N T G * Y R C F S V T G E Y S T K S F * E * C M R R P S C S C P A S I R D N TTCTACGAAAAGACACTGACCACTCATGAGTTGGTTCAGTAAGACTCTTATCACATACGCCGCTGGCTCAACGAGAACGGGCCGCAGTTATGCCCTATTA XmnI ACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGA < 2700 P R H I A E L * K C S S L E N V L R G E N S Q G S Y R C * D P V R R A T * Q N F K S A H H W K T F F G A K T L K D L T A V E I Q F D T A P H S R T L K V L I I G K R S S G R K L S R I L P L L R S S S M TGGCGCGGTGTATCGTCTTGAAATTTTCACGAGTAGTAACCTTTTGCAAGAAGCCCCGCTTTTGAGAGTTCCTAGAATGGCGACAACTCTAGGTCAAGCT TGTAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGG < 2800 C N P L V H P T D L Q H L L L S P A F L G E Q K Q E G K M P Q K R E V T H S C T Q L I F S I F Y F H Q R F W V S K N R K A K C R K K G * P T R A P N * S S A S F T F T S V S G * A K T G R Q N A A K K G ACATTGGGTGAGCACGTGGGTTGACTAGAAGTCGTAGAAAATGAAAGTGGTCGCAAAGACCCACTCGTTTTTGTCCTTCCGTTTTACGGCGTTTTTTCCC AATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGTCTCATGAGCGGATACATATTT < 2900 * G R H G N V E Y S Y S S F F N I I E A F I R V I V S * A D T Y L N K G D T E M L N T H T L P F S I L L K H L S G L L S H E R I H I * I R A T R K C * I L I L F L F Q Y Y * S I Y Q G Y C L M S G Y I F 6

7 TTATTCCCGCTGTGCCTTTACAACTTATGAGTATGAGAAGGAAAAAGTTATAATAACTTCGTAAATAGTCCCAATAACAGAGTACTCGCCTATGTATAAA GAATGTATTTAGAAAAATAAACAAATAGGGGTTCCGCGCACATTTCCCCGAAAAGTGCCAC < 2961 N V F R K I N K * G F R A H F P E K C H M Y L E K * T N R G S A H I S P K S A X E C I * K N K Q I G V P R T F P R K V P X CTTACATAAATCTTTTTATTTGTTTATCCCCAAGGCGCGTGTAAAGGGGCTTTTCACGGTG Features : T3 M13-fwd M13-rev T7 ColE1 origin F1 ori LacZ alpha LacO AmpR : [790 : CCW] : [599 : CW] : [828 : CCW] : [626 : CW] : [1824 : CCW] : [13 : CW] : [528 : CCW] : [856 : CCW] : [2635 : CCW] V. File Format Serial Cloner uses an extended DNA Strider file format. It is still readable by DNA Strider and by any software that respects the recommendations of the DNA Strider format. Strider will just ignore additional information, and in particular features and annotations. Of course, if one then saves the sequence using DNA Strider for example, Feature data will be lost. Serial Cloner 2.1 can now export file sequence in a GenBank format that will contain the Annotations/Features. Special Serial_Cloner fields that will, for example, contain the color associated with the Feature, will be present. These fields will of course be properly parsed by Serial Cloner. VI. Import of feature-enriched sequences Serial Cloner 2.x imports features-containing sequences saved by ApE or Vector NTI. Feature colors should be correctly imported. With Version 2.1 of Serial Cloner, I also provide with the MacOS version a companion Software created by Davide Cittaro that will transform a MacVector file to a GenBank formatted file (see the short description in the Companion Software_Read-Me.pdf file). This Genbank format will be read by Serial Cloner. Import of Genbank and EMBL have been improved and features should now be recognized and parsed. This is true for sequences saved in files or imported from the Genbank/EMBL web interface using Serial Cloner mini-web Browser (using its bottomleft button). See the example bellow. [Note that other formats devoid of Features are still recognized by Serial Cloner : Fasta, pdraw32, raw text]. Some Features are still ignored (like the join Feature) as no splicing tools are yet available in Serial Cloner. Note that when Serial Cloner opens or paste a Sequence that was in an external format, a message will indicate that a particularly formatted sequence has been recognized. It is possible to prevent such a message from showing, which may be useful if you often open such external files (for example if you systematically open Vector NTI files). 7

8 The pegfp-c1 has been obtained from the NCBI web interface using Serial Cloner mini-web Browser. Because a GenBank formatted sequence has been detected by Serial Cloner, the button "Create a New Sequence Window " at the bottom left was enabled. Clicking on it imported the Genbank entry in a new Sequence Window, correctly parsing the Features. VII. Copy/Paste A. Copying There are several way to copy a sequence in Serial Cloner; some will keep Feature information. - Copy (shortcut : [C]-C) : this is a basic Copy function. The selected portion of the sequence will be copied in the Clipboard and no Feature information will be kept. 8

9 Ex: copying between 12 and 1840 of pbluescript II SK (+): GCGTTAATATTTTGTTAAAATTCGCGTTAAATTTTTGTTAAATCAGCTCATTTTTTAACCAATAGGCCGAAATCGGCAAA ATCCCTTATAAATCAAAAGAATAGACCGAGATAGGGTTGAGTGTTGTTCCAGTTTGGAACAAGAGTCCACTATTAAAGAA CGTGGACTCCAACGTCAAAGGGCGAAAAACCGTCTATCAGGGCGATGGCCCACTACGTGAACCATCACCCTAATCAAGTT TTTTGGGGTCGAGGTGCCGTAAAGCACTAAATCGGAACCCTAAAGGGAGCCCCCGATTTAGAGCTTGACGGGGAAAGCCG GCGAACGTGGCGAGAAAGGAAGGGAAGAAAGCGAAAGGAGCGGGCGCTAGGGCGCTGGCAAGTGTAGCGGTCACGCTGCG CGTAACCACCACACCCGCCGCGCTTAATGCGCCGCTACAGGGCGCGTCCCATTCGCCATTCAGGCTGCGCAACTGTTGGG AAGGGCGATCGGTGCGGGCCTCTTCGCTATTACGCCAGCTGGCGAAAGGGGGATGTGCTGCAAGGCGATTAAGTTGGGTA ACGCCAGGGTTTTCCCAGTCACGACGTTGTAAAACGACGGCCAGTGAGCGCGCGTAATACGACTCACTATAGGGCGAATT GGGTACCGGGCCCCCCCTCGAGGTCGACGGTATCGATAAGCTTGATATCGAATTCCTGCAGCCCGGGGGATCCACTAGTT CTAGAGCGGCCGCCACCGCGGTGGAGCTCCAGCTTTTGTTCCCTTTAGTGAGGGTTAATTGCGCGCTTGGCGTAATCATG GTCATAGCTGTTTCCTGTGTGAAATTGTTATCCGCTCACAATTCCACACAACATACGAGCCGGAAGCATAAAGTGTAAAG CCTGGGGTGCCTAATGAGTGAGCTAACTCACATTAATTGCGTTGCGCTCACTGCCCGCTTTCCAGTCGGGAAACCTGTCG TGCCAGCTGCATTAATGAATCGGCCAACGCGCGGGGAGAGGCGGTTTGCGTATTGGGCGCTCTTCCGCTTCCTCGCTCAC TGACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGGTAATACGGTTATCCACAGAAT CAGGGGATAACGCAGGAAAGAACATGTGAGCAAAAGGCCAGCAAAAGGCCAGGAACCGTAAAAAGGCCGCGTTGCTGGCG TTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACT ATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGT CCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGC TCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAA CCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTA CAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTT ACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCA GCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCA - Copy as Fasta (shortcut : [C]-K) : The selected portion of the sequence will be copied in the Clipboard in a Fasta format Ex: copying between 12 and 1840 of pbluescript II SK (+): > [pbluescript II SK(+) bp] gi emb X52328 ARBL2SKP pbluescript II SK(+) vector DNA, phagemid excised from lambda ZAPII - Selection From [12] To [1840] GCGTTAATATTTTGTTAAAATTCGCGTTAAATTTTTGTTAAATCAGCTCATTTTTTAACCAATAGGCCGAAATCGGCAAA ATCCCTTATAAATCAAAAGAATAGACCGAGATAGGGTTGAGTGTTGTTCCAGTTTGGAACAAGAGTCCACTATTAAAGAA CGTGGACTCCAACGTCAAAGGGCGAAAAACCGTCTATCAGGGCGATGGCCCACTACGTGAACCATCACCCTAATCAAGTT TTTTGGGGTCGAGGTGCCGTAAAGCACTAAATCGGAACCCTAAAGGGAGCCCCCGATTTAGAGCTTGACGGGGAAAGCCG GCGAACGTGGCGAGAAAGGAAGGGAAGAAAGCGAAAGGAGCGGGCGCTAGGGCGCTGGCAAGTGTAGCGGTCACGCTGCG CGTAACCACCACACCCGCCGCGCTTAATGCGCCGCTACAGGGCGCGTCCCATTCGCCATTCAGGCTGCGCAACTGTTGGG AAGGGCGATCGGTGCGGGCCTCTTCGCTATTACGCCAGCTGGCGAAAGGGGGATGTGCTGCAAGGCGATTAAGTTGGGTA ACGCCAGGGTTTTCCCAGTCACGACGTTGTAAAACGACGGCCAGTGAGCGCGCGTAATACGACTCACTATAGGGCGAATT GGGTACCGGGCCCCCCCTCGAGGTCGACGGTATCGATAAGCTTGATATCGAATTCCTGCAGCCCGGGGGATCCACTAGTT CTAGAGCGGCCGCCACCGCGGTGGAGCTCCAGCTTTTGTTCCCTTTAGTGAGGGTTAATTGCGCGCTTGGCGTAATCATG GTCATAGCTGTTTCCTGTGTGAAATTGTTATCCGCTCACAATTCCACACAACATACGAGCCGGAAGCATAAAGTGTAAAG CCTGGGGTGCCTAATGAGTGAGCTAACTCACATTAATTGCGTTGCGCTCACTGCCCGCTTTCCAGTCGGGAAACCTGTCG TGCCAGCTGCATTAATGAATCGGCCAACGCGCGGGGAGAGGCGGTTTGCGTATTGGGCGCTCTTCCGCTTCCTCGCTCAC TGACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGGTAATACGGTTATCCACAGAAT CAGGGGATAACGCAGGAAAGAACATGTGAGCAAAAGGCCAGCAAAAGGCCAGGAACCGTAAAAAGGCCGCGTTGCTGGCG TTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACT ATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGT CCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGC TCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAA CCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTA CAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTT ACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCA GCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCA Note that the "Copy all sequence as Fasta" will copy all opened sequence in Fasta and join them in the Clipboard. This format is useful when multi-aligning sequences (form exemple using CLUSTAL). 9

10 - Copy Formatted (shortcut : [C]-[SHIFT]-K) The full sequence will be copied as a Fasta-formatted sequence. Features will be shown in their colors and a legend will be added at the end of the sequence. Ex: copying the sequence of pbluescript II SK (+): > [pbluescript II SK(+) bp] gi emb X52328 ARBL2SKP pbluescript II SK(+) vector DNA, phagemid excised from lambda ZAPII CTAAATTGTAAGCGTTAATATTTTGTTAAAATTCGCGTTAAATTTTTGTTAAATCAGCTCATTTTTTAACCAATAGGCCG AAATCGGCAAAATCCCTTATAAATCAAAAGAATAGACCGAGATAGGGTTGAGTGTTGTTCCAGTTTGGAACAAGAGTCCA CTATTAAAGAACGTGGACTCCAACGTCAAAGGGCGAAAAACCGTCTATCAGGGCGATGGCCCACTACGTGAACCATCACC CTAATCAAGTTTTTTGGGGTCGAGGTGCCGTAAAGCACTAAATCGGAACCCTAAAGGGAGCCCCCGATTTAGAGCTTGAC GGGGAAAGCCGGCGAACGTGGCGAGAAAGGAAGGGAAGAAAGCGAAAGGAGCGGGCGCTAGGGCGCTGGCAAGTGTAGCG GTCACGCTGCGCGTAACCACCACACCCGCCGCGCTTAATGCGCCGCTACAGGGCGCGTCCCATTCGCCATTCAGGCTGCG CAACTGTTGGGAAGGGCGATCGGTGCGGGCCTCTTCGCTATTACGCCAGCTGGCGAAAGGGGGATGTGCTGCAAGGCGAT TAAGTTGGGTAACGCCAGGGTTTTCCCAGTCACGACGTTGTAAAACGACGGCCAGTGAGCGCGCGTAATACGACTCACTA TAGGGCGAATTGGGTACCGGGCCCCCCCTCGAGGTCGACGGTATCGATAAGCTTGATATCGAATTCCTGCAGCCCGGGGG ATCCACTAGTTCTAGAGCGGCCGCCACCGCGGTGGAGCTCCAGCTTTTGTTCCCTTTAGTGAGGGTTAATTGCGCGCTTG GCGTAATCATGGTCATAGCTGTTTCCTGTGTGAAATTGTTATCCGCTCACAATTCCACACAACATACGAGCCGGAAGCAT AAAGTGTAAAGCCTGGGGTGCCTAATGAGTGAGCTAACTCACATTAATTGCGTTGCGCTCACTGCCCGCTTTCCAGTCGG GAAACCTGTCGTGCCAGCTGCATTAATGAATCGGCCAACGCGCGGGGAGAGGCGGTTTGCGTATTGGGCGCTCTTCCGCT TCCTCGCTCACTGACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGGTAATACGGTT ATCCACAGAATCAGGGGATAACGCAGGAAAGAACATGTGAGCAAAAGGCCAGCAAAAGGCCAGGAACCGTAAAAAGGCCG CGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAAC CCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTAC CGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGT AGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGT CTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGT AGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGC TGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTT GTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCA GTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAA AATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCT ATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTT ACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAG CCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGA GTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTTGG TATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCT CCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCT CTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCG GCGACCGAGTTGCTCTTGCCCGGCGTCAATACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTG GAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACCC AACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGG AATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGTC TCATGAGCGGATACATATTTGAATGTATTTAGAAAAATAAACAAATAGGGGTTCCGCGCACATTTCCCCGAAAAGTGCCA C Features : T3 M13-fwd M13-rev T7 ColE1 origin F1 ori LacZ alpha LacO AmpR : [790 : CCW] : [599 : CW] : [828 : CCW] : [626 : CW] : [1824 : CCW] : [13 : CW] : [528 : CCW] : [856 : CCW] : [2635 : CCW] - Copy as GenBank The full sequence will be copied as a GenBank formatted sequence. One interesting use of such a format is to paste it in a database (FileMaker, Excel, etc ) so that anybody in the lab can import the sequence with its features by copying the text back into Serial Cloner. The format is exactly the same than the one saved using the Export as Genbank function. 10

11 Ex: copying the sequence of pbluescript II SK (+): LOCUS pbluescript_ii_sk(+) 2961 bp DNA circular 02/05/10 DEFINITION ACCESSION VERSION SOURCE ORGANISM COMMENT Serial Cloner Genbank Format COMMENT SerialCloner_Type=DNA COMMENT SerialCloner_Comments=gi emb X52328 ARBL2SKP pbluescript II SK(+) vector DNA, phagemid excised from lambda ZAPII COMMENT SerialCloner_Ends=0,0,,0, FEATURES primer_bind ORIGIN Location/Qualifiers complement( ) /label=t3 /SerialCloner_Color=&h008B8B /SerialCloner_Show=True /SerialCloner_Protect=False /SerialCloner_Arrow=True primer_bind /label=m13-fwd /SerialCloner_Color=&h008B8B /SerialCloner_Show=True /SerialCloner_Protect=False /SerialCloner_Arrow=True primer_bind complement( ) /label=m13-rev /SerialCloner_Color=&h008B8B /SerialCloner_Show=True /SerialCloner_Protect=False /SerialCloner_Arrow=True primer_bind /label=t7 /SerialCloner_Color=&h008B8B /SerialCloner_Show=True /SerialCloner_Protect=False /SerialCloner_Arrow=True rep_origin complement( ) /label=cole1 origin /SerialCloner_Color=&h4682B4 /SerialCloner_Show=True /SerialCloner_Protect=False /SerialCloner_Arrow=True rep_origin /label=f1 ori /SerialCloner_Color=&hFF8000 /SerialCloner_Show=True /SerialCloner_Protect=True /SerialCloner_Arrow=True CDS misc_binding CDS complement( ) /label=lacz alpha /SerialCloner_Color=&h6495ED /SerialCloner_Show=True /SerialCloner_Protect=False /SerialCloner_Arrow=True complement( ) /label=laco /SerialCloner_Color=&h6495ED /SerialCloner_Show=True /SerialCloner_Protect=False /SerialCloner_Arrow=True complement( ) /label=ampr /SerialCloner_Color=&h8FBC8F /SerialCloner_Show=True /SerialCloner_Protect=False /SerialCloner_Arrow=True 1 CTAAATTGTA AGCGTTAATA TTTTGTTAAA ATTCGCGTTA AATTTTTGTT AAATCAGCTC 11

12 // 61 ATTTTTTAAC CAATAGGCCG AAATCGGCAA AATCCCTTAT AAATCAAAAG AATAGACCGA 121 GATAGGGTTG AGTGTTGTTC CAGTTTGGAA CAAGAGTCCA CTATTAAAGA ACGTGGACTC 181 CAACGTCAAA GGGCGAAAAA CCGTCTATCA GGGCGATGGC CCACTACGTG AACCATCACC 241 CTAATCAAGT TTTTTGGGGT CGAGGTGCCG TAAAGCACTA AATCGGAACC CTAAAGGGAG 301 CCCCCGATTT AGAGCTTGAC GGGGAAAGCC GGCGAACGTG GCGAGAAAGG AAGGGAAGAA 361 AGCGAAAGGA GCGGGCGCTA GGGCGCTGGC AAGTGTAGCG GTCACGCTGC GCGTAACCAC 421 CACACCCGCC GCGCTTAATG CGCCGCTACA GGGCGCGTCC CATTCGCCAT TCAGGCTGCG 481 CAACTGTTGG GAAGGGCGAT CGGTGCGGGC CTCTTCGCTA TTACGCCAGC TGGCGAAAGG 541 GGGATGTGCT GCAAGGCGAT TAAGTTGGGT AACGCCAGGG TTTTCCCAGT CACGACGTTG 601 TAAAACGACG GCCAGTGAGC GCGCGTAATA CGACTCACTA TAGGGCGAAT TGGGTACCGG 661 GCCCCCCCTC GAGGTCGACG GTATCGATAA GCTTGATATC GAATTCCTGC AGCCCGGGGG 721 ATCCACTAGT TCTAGAGCGG CCGCCACCGC GGTGGAGCTC CAGCTTTTGT TCCCTTTAGT 781 GAGGGTTAAT TGCGCGCTTG GCGTAATCAT GGTCATAGCT GTTTCCTGTG TGAAATTGTT 841 ATCCGCTCAC AATTCCACAC AACATACGAG CCGGAAGCAT AAAGTGTAAA GCCTGGGGTG 901 CCTAATGAGT GAGCTAACTC ACATTAATTG CGTTGCGCTC ACTGCCCGCT TTCCAGTCGG 961 GAAACCTGTC GTGCCAGCTG CATTAATGAA TCGGCCAACG CGCGGGGAGA GGCGGTTTGC 1021 GTATTGGGCG CTCTTCCGCT TCCTCGCTCA CTGACTCGCT GCGCTCGGTC GTTCGGCTGC 1081 GGCGAGCGGT ATCAGCTCAC TCAAAGGCGG TAATACGGTT ATCCACAGAA TCAGGGGATA 1141 ACGCAGGAAA GAACATGTGA GCAAAAGGCC AGCAAAAGGC CAGGAACCGT AAAAAGGCCG 1201 CGTTGCTGGC GTTTTTCCAT AGGCTCCGCC CCCCTGACGA GCATCACAAA AATCGACGCT 1261 CAAGTCAGAG GTGGCGAAAC CCGACAGGAC TATAAAGATA CCAGGCGTTT CCCCCTGGAA 1321 GCTCCCTCGT GCGCTCTCCT GTTCCGACCC TGCCGCTTAC CGGATACCTG TCCGCCTTTC 1381 TCCCTTCGGG AAGCGTGGCG CTTTCTCATA GCTCACGCTG TAGGTATCTC AGTTCGGTGT 1441 AGGTCGTTCG CTCCAAGCTG GGCTGTGTGC ACGAACCCCC CGTTCAGCCC GACCGCTGCG 1501 CCTTATCCGG TAACTATCGT CTTGAGTCCA ACCCGGTAAG ACACGACTTA TCGCCACTGG 1561 CAGCAGCCAC TGGTAACAGG ATTAGCAGAG CGAGGTATGT AGGCGGTGCT ACAGAGTTCT 1621 TGAAGTGGTG GCCTAACTAC GGCTACACTA GAAGGACAGT ATTTGGTATC TGCGCTCTGC 1681 TGAAGCCAGT TACCTTCGGA AAAAGAGTTG GTAGCTCTTG ATCCGGCAAA CAAACCACCG 1741 CTGGTAGCGG TGGTTTTTTT GTTTGCAAGC AGCAGATTAC GCGCAGAAAA AAAGGATCTC 1801 AAGAAGATCC TTTGATCTTT TCTACGGGGT CTGACGCTCA GTGGAACGAA AACTCACGTT 1861 AAGGGATTTT GGTCATGAGA TTATCAAAAA GGATCTTCAC CTAGATCCTT TTAAATTAAA 1921 AATGAAGTTT TAAATCAATC TAAAGTATAT ATGAGTAAAC TTGGTCTGAC AGTTACCAAT 1981 GCTTAATCAG TGAGGCACCT ATCTCAGCGA TCTGTCTATT TCGTTCATCC ATAGTTGCCT 2041 GACTCCCCGT CGTGTAGATA ACTACGATAC GGGAGGGCTT ACCATCTGGC CCCAGTGCTG 2101 CAATGATACC GCGAGACCCA CGCTCACCGG CTCCAGATTT ATCAGCAATA AACCAGCCAG 2161 CCGGAAGGGC CGAGCGCAGA AGTGGTCCTG CAACTTTATC CGCCTCCATC CAGTCTATTA 2221 ATTGTTGCCG GGAAGCTAGA GTAAGTAGTT CGCCAGTTAA TAGTTTGCGC AACGTTGTTG 2281 CCATTGCTAC AGGCATCGTG GTGTCACGCT CGTCGTTTGG TATGGCTTCA TTCAGCTCCG 2341 GTTCCCAACG ATCAAGGCGA GTTACATGAT CCCCCATGTT GTGCAAAAAA GCGGTTAGCT 2401 CCTTCGGTCC TCCGATCGTT GTCAGAAGTA AGTTGGCCGC AGTGTTATCA CTCATGGTTA 2461 TGGCAGCACT GCATAATTCT CTTACTGTCA TGCCATCCGT AAGATGCTTT TCTGTGACTG 2521 GTGAGTACTC AACCAAGTCA TTCTGAGAAT AGTGTATGCG GCGACCGAGT TGCTCTTGCC 2581 CGGCGTCAAT ACGGGATAAT ACCGCGCCAC ATAGCAGAAC TTTAAAAGTG CTCATCATTG 2641 GAAAACGTTC TTCGGGGCGA AAACTCTCAA GGATCTTACC GCTGTTGAGA TCCAGTTCGA 2701 TGTAACCCAC TCGTGCACCC AACTGATCTT CAGCATCTTT TACTTTCACC AGCGTTTCTG 2761 GGTGAGCAAA AACAGGAAGG CAAAATGCCG CAAAAAAGGG AATAAGGGCG ACACGGAAAT 2821 GTTGAATACT CATACTCTTC CTTTTTCAAT ATTATTGAAG CATTTATCAG GGTTATTGTC 2881 TCATGAGCGG ATACATATTT GAATGTATTT AGAAAAATAA ACAAATAGGG GTTCCGCGCA 2941 CATTTCCCCG AAAAGTGCCA C B. Pasting When pasting a sequence in a Sequence Window, Serial Cloner tries to guess the format (Fasta, Generic GenBank, Serial Cloner GenBank) and to parse the data, including the Features present in a GenBank format. Note that it is even possible to copy a full web page that contains a GenBank entry (from Safari or Firefox for example) and to paste it directly in a Sequence Field. It should be properly parsed (Sequence, comments, Features). As indicated above, copying and pasting sequences in Genbank Serial Cloner Format is also a good way to store and share annotated sequence in a text format that can be imported later in Serial Cloner by any user. 12

13 If Serial Cloner cannot detect a particular format, then it will parse it as a raw text filtering out non-atgc letter (in a DNA window) or non-degenerate DNA letters (in a Degenerate DNA window). VIII. Adding Features to a Sequence Several ways exist to add new Features to a sequence. A. Manual entry Simply go in the Feature section (Features Tab) and press the '+' button. Then, enter numerically the coordinates of the feature and set the different values. If a portion of sequence has been selected in the Sequence Field before pressing the '+' button, then the coordinates of the current selection will be automatically proposed as default values for the features (and in some cases the translation pasted as indicated bellow). B. After selecting a nucleotide fragment in the sequence window. First select a portion of sequence in the sequence window either directly or using the ORF search for example. Then either display a contextual menu (Right-Click or [CTRL]- Click) and select 'Create New Feature From Selection'. Alternatively, use the 'New Feature From Selection' (shortcut : [C]-@) from the 'Features' menu. Note that if the 'Selection information and Translation' was shown before creating the Feature, then the current translation will be added in the features comments (see screenshots bellow). 13

14 C. After selecting a nucleotide fragment in the Graphic Window. First, select a fragment by choosing an upstream (simple click) and downstream (doubleclick or [SHIFT]-Click) restriction site. Clockwise and Counter-Clockwise can be toggled using the spacebar. Then display a contextual menu by right-clicking (or [CTRL]-Clicking) on the map and select 'Make New Feature'. Alternatively, use the 'New Feature From Selection' (shortcut : [C]-@) from the 'Features' menu. The feature will created between these two sites and the names of the enzymes added in the comment field. The Feature will contain the restriction sites used at each end. 14

15 D. By automatic scanning Serial Cloner now includes a database that allows to automatically detect the presence of frequent sequences like the β-lactamase, the ColE1 or the f1 sequence. By default, Serial Cloner comes with tens of pre-defined Features (see the list bellow). A new interface is provided in Serial Cloner 2.1 that allows the addition of user-defined sequences. To use the database and detects the presence of these domains in your sequences, simply use the Scan button present in the Toolbar or the use the 'Scan Sequence' command ([ALT]-[C]-S, in the 'Features' menu). This can be done either while displaying the Sequence Window, the Graphic Map. In the latter case, the associated Sequence Window must not have been closed. It is also allowed to scan in the Build a Construct window. Since V2.1, it is also possible to scan directly in the Sequence Map window. It is also possible to scan using the 'Scan' button present it the 'Features' tab of the Sequence Window. By default, all are 'Shown' but the 'Show' checkbox can be use to alter this state. Note that if you scan more than once the same sequence, the same Features will of course be found and the new Features will replace the identical new ones. BUT if you change something on an automatically found annotation (like its name, color, etc.), it will not anymore be automatically erased upon a new scan (to protect your modifications). A new scan will thus result in a duplication of this Feature and the unwanted one will have to be deleted manually. IX. Add/Delete/Modify Features to be scanned for A. Manage Feature interface. The new Feature menu proposes a 'Manage Features ' command. It will open a new window that will allow to add/delete/modify Features and Feature collections. It can be used for 'Simple' definition or 'Complex' definition of Features. 15

16 a. Feature Collections On the left are listed the different Collections. The checkbox indicates whether this Collection should be used when scanning or not. As scan time depends on the number of Features to scan for, it is a good idea to unselect a Collection that does not correspond to the work you routinely carry-out if scanning time starts to bother you. Note that you can also delete the Collection but this will not be undoable so it may be safer to simply unselect it. Also, even in Collection you want to use for scanning, some Features will never be meaningful for your work. What you can do is to create a new Collection (named for example 'Ignored Features') and store the Features you currently never use in this Collection. To change the Collection to which a Feature belong, use the button under 'Collection' (on the right) and select another one. Following the same track, it is possible to have a Feature present in two different Collections. Simply Duplicate the Feature (button 'Duplicate') and change the Collection associated to the duplicated one. You can thus create Collections of Features that you only scan in certain circumstances (for example if you want, sometimes, to indicate all the Cysteines in a sequence or all the 'ATG', or the NcoI and NotI sites, etc ). b. Import a Feature Collection You can also import Feature Collections either saved by Serial Cloner, by other software, or simply organized as a table. External Collections can be either in an ApE format or generic. The format is described in the Import Window. If you want to send your Feature Collections to a colleague, you can use the Export command (see bellow). Note also that the Feature Collections are stored in ~/Library/Application Support/SerialCloner/Features/ (MacOSX) or Users/~/AppData/Roaming/SerialCloner/Features/ (Windows 7) or \Documents and Settings\Admin\Application Data\SerialCloner\Features (Windows XP) ['Admin' may be replaced by a username in certain system config). 16

17 c. Export a Feature Collection It is possible to export the currently selected Feature Collection and save it independently. This may be useful to share a special Feature Collection with your colleagues. You can also use this export function to send me a Collection of Feature that you want to share with the community. I will put them for download in the Serial Cloner Web site. To Export, press the [ALT] key. The 'Import' button will be replaced by an 'Export' button. The Feature Collection will be saved in the Serial Cloner format. d. Feature List The second list displays the Features contained in the currently selected Collection. It is possible to search for a Feature inside this collection using the search field. As for the Feature Collection before, the Checkbox indicates whether the Feature should be used when scanning. Buttons under the list allows addition or deletion of Features. Be careful, there is no undo. It may be safer just to uncheck the Feature in general if you do not want to scan for it. It is also possible to duplicate a Feature. This can be useful when generating a series of very similar Features or when one Features is to be stored in different collections that will not be scanned at the same time. e. Feature definition The right side of the window allows users to enter Feature details. Name fields are explicit and should be easy to understand in the 'Simple' definition mode. It is possible to change the collection the Feature is attached to here. Note also that Features can be entered in DNA or Protein mode. In the former mode, degenerate nucleotide alphabet can be used. The Protein mode is particularly interesting for tags and protease cleavage sites since different codon bias may have been used in different constructs. Look at the 'Tag & Cut' Collection for examples. Note also that it is also to impose scanning only in the sense strand. The 'Complex' mode may require more explanations. 17

18 - 5' Sequence of the Feature : if used alone, it is the exact equivalent of the Sequence of the Feature used in the 'Simple' definition mode. When used with the 3' field mode (see bellow), it will determine the consensus of the 5' end of the sequence - 3' Sequence of the Feature : Indicates the sequence of the 3' end of the Feature. Any intervening sequence present between the 5' and the 3' sequence of the Feature will be considered as part of the Feature. Serial Cloner will look for : [5' Sequence ]-NNNNN-[3' Sequence] - Potential 5' and 3' sequences : these sequences may or may not be present in the sequence to be scanned. If present, they will be incorporated to the detected Feature upon scanning. Good examples are the START and STOP codons of the EGFP that are not always present (depending of Nter or Cter fusion) but that belong to the Feature when present. - Sequence Upstream and Downstream of the Feature : Indicates sequences that must be present for the Feature to be scored as 'detected' when scanning, but that do not belong to the Feature itself. A good example is a particular amino-acid that should be highlighted if present in a certain context but not always (like the cystein in the CVLL sequence). Following this track, we plan to allow users to enter complex consensus sequences in the future (like [S/T]X[RK]). 18

19 Serial Cloner 2.1 : Internal database of Features The following features will be looked for upon scanning. Note that proper detection depends on correct matching to the consensus sequence stored in Serial Cloner. Please, do not hesitate to signal any lack of detection so that I can update the consensus sequence for this Feature. You can also propose to add your preferred Feature in the database (submitting by a consensus sequence or a Collection). If I received enough of them, I will put them on my Web site for user to download it or incorporate them in a future version of Serial Cloner. Internal Database : A. Generic: T3 M13-fwd M13-rev T7 SP6 ColE1 origin F1 ori 2u ori M13 origin LacZ alpha LacO AmpR LacI Kan/neoR KanR CmR TetR TetR ZeoR BlastiR PuroR TetA GentaR HygroR SV40 late polya CMV promoter SV40 early promoter hgh polya signal FRT LoxP TRE U6 promoter EM7 promoter mpgk Prom bar 19

20 Spec dhfr APH(3')-IIA aada tsr pat aph orivr6kgamma oris orirg R6K ori 35S CMV PBAD AML-P NOS-P TrpC CaMV 35S mpgk Prom EGFP GST mrfp1 mcherry EYFP ECFP hrluc1 Rluc AcGFP IRES [1] IRES [2] Amp Promoter Lac Promoter HIV-1 5LTR HIV-1 psi HIV RRE Delta U3 SV40 intron Synthetic intron SV40 ORI laci tac promoter rrnb rrnb T1 rrnbt2 bgh PA B. Yeast 20

21 KanMX URA3 TRP1 MET15 LYS2 LEU2 HIS3 ADE2 2 micron origin CEN-ARS prs CEN-ARS YCp-lac CEN-ARS YCp50 GAL4 terminator CYC1 terminator ADH1 terminator MET15 promoter GAL1-10 promoter GAL1 promoter ADH1 promoter Gal4 activation domain LexA DNA-binding domain Gal4 DNA-binding domain HIS1 PDR5 C. Other IL2 ss human IgG1 Fc human IgG2 Fc human IgG3 Fc human IgG4 Fc mouse IgG2A Fc mouse IgG2B Fc mouse IgG3 Fc rabbit IgG Fc rat IgG2B Fc D. Tags & Cut 6His Cys C-Myc tag HA tag VSV-G tag HSV tag Flag tag T7 tag 21

22 GluGlu tag E- tag S-tag PC tag Strp tag II SBP tag Avitag TEV tag [1] TEV tag [2] PreScission site Factor Xa site Thrombin site SV40 NLS1 SV40 NLS2 E. Gateway attb4 attb3 AttB2 AttB1 attp4 attp3 AttP2 AttP1 attl4 attl3 AttL2 AttL1 attr4 attr3 AttR2 AttR1 ccdb 22